Graph polynomials is one of the important research directions in mathematical chemistry. The coefficients of some graph polynomials, such as matching polynomial and permanental polynomial, are related to structural properties of graphs. The Hosoya index of a graph is the sum of the absolute value of all coefficients for the matching polynomial. And the permanental sum of a graph is the sum of the absolute value of all coefficients of the permanental polynomial. In this paper, we characterize the second to sixth minimal Hosoya indices of all bicyclic graphs. Furthermore, using the results, the second to sixth minimal permanental sums of all bicyclic graphs are also characterized.